Back to Multiple platform build/check report for BioC 3.17 |
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This page was generated on 2023-04-12 10:55:34 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
To the developers/maintainers of the benchdamic package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/benchdamic.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
Package 153/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
benchdamic 1.5.2 (landing page) Matteo Calgaro
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ||||||||||
Package: benchdamic |
Version: 1.5.2 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:benchdamic.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings benchdamic_1.5.2.tar.gz |
StartedAt: 2023-04-12 04:52:02 -0400 (Wed, 12 Apr 2023) |
EndedAt: 2023-04-12 05:24:36 -0400 (Wed, 12 Apr 2023) |
EllapsedTime: 1953.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: benchdamic.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:benchdamic.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings benchdamic_1.5.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/benchdamic.Rcheck’ * using R Under development (unstable) (2023-02-14 r83833) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 * running under: Ubuntu 20.04.6 LTS * using session charset: UTF-8 * checking for file ‘benchdamic/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘benchdamic’ version ‘1.5.2’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘benchdamic’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘intro.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: OK
benchdamic.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL benchdamic ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’ * installing *source* package ‘benchdamic’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (benchdamic)
benchdamic.Rcheck/tests/testthat.Rout
R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(benchdamic) > > test_check("benchdamic") |------------(25%)----------(50%)----------(75%)----------| |------------(25%)----------(50%)----------(75%)----------| |------------(25%)----------(50%)----------(75%)----------| |------------(25%)----------(50%)----------(75%)----------| |------------(25%)----------(50%)----------(75%)----------| [ FAIL 0 | WARN 1 | SKIP 0 | PASS 292 ] [ FAIL 0 | WARN 1 | SKIP 0 | PASS 292 ] > > proc.time() user system elapsed 69.659 3.515 87.846
benchdamic.Rcheck/benchdamic-Ex.timings
name | user | system | elapsed | |
CAT | 0.005 | 0.000 | 0.005 | |
DA_ALDEx2 | 3.619 | 0.116 | 3.736 | |
DA_ANCOM | 1.414 | 0.080 | 1.495 | |
DA_DESeq2 | 4.001 | 0.096 | 4.097 | |
DA_MAST | 0.582 | 0.012 | 0.594 | |
DA_NOISeq | 1.512 | 0.048 | 1.561 | |
DA_Seurat | 0.777 | 0.004 | 0.781 | |
DA_basic | 0.028 | 0.000 | 0.027 | |
DA_corncob | 1.116 | 0.012 | 1.137 | |
DA_dearseq | 0.140 | 0.004 | 0.144 | |
DA_edgeR | 0.160 | 0.000 | 0.161 | |
DA_limma | 0.065 | 0.000 | 0.066 | |
DA_metagenomeSeq | 0.257 | 0.000 | 0.256 | |
RMSE | 0.001 | 0.000 | 0.000 | |
addKnowledge | 0.159 | 0.000 | 0.158 | |
areaCAT | 3.729 | 0.048 | 3.776 | |
checkNormalization | 0.001 | 0.000 | 0.000 | |
createColors | 0.005 | 0.000 | 0.004 | |
createConcordance | 4.276 | 0.072 | 4.348 | |
createEnrichment | 0.242 | 0.000 | 0.241 | |
createMocks | 0.002 | 0.001 | 0.002 | |
createPositives | 0.783 | 0.006 | 0.790 | |
createSplits | 0.028 | 0.000 | 0.028 | |
createTIEC | 2.520 | 0.044 | 2.564 | |
enrichmentTest | 0.152 | 0.000 | 0.152 | |
extractDA | 0.168 | 0.000 | 0.168 | |
extractStatistics | 0.166 | 0.000 | 0.167 | |
fitDM | 0.029 | 0.000 | 0.029 | |
fitHURDLE | 0.353 | 0.004 | 0.357 | |
fitModels | 1.231 | 0.036 | 1.266 | |
fitNB | 0.043 | 0.000 | 0.043 | |
fitZIG | 0.052 | 0.000 | 0.052 | |
fitZINB | 0.433 | 0.008 | 0.441 | |
getDA | 0.069 | 0.008 | 0.078 | |
getPositives | 0.081 | 0.000 | 0.081 | |
getStatistics | 0.058 | 0.008 | 0.066 | |
get_counts_metadata | 0.221 | 0.000 | 0.221 | |
iterative_ordering | 0.01 | 0.00 | 0.01 | |
meanDifferences | 0.002 | 0.000 | 0.001 | |
norm_CSS | 0.072 | 0.000 | 0.072 | |
norm_DESeq2 | 0.446 | 0.000 | 0.446 | |
norm_TSS | 0.046 | 0.000 | 0.046 | |
norm_edgeR | 0.036 | 0.000 | 0.036 | |
plotConcordance | 4.738 | 0.112 | 4.850 | |
plotContingency | 1.067 | 0.000 | 1.068 | |
plotEnrichment | 1.071 | 0.000 | 1.071 | |
plotFDR | 2.073 | 0.004 | 2.076 | |
plotFPR | 2.079 | 0.008 | 2.088 | |
plotKS | 2.067 | 0.028 | 2.095 | |
plotLogP | 2.196 | 0.016 | 2.213 | |
plotMD | 2.673 | 0.028 | 2.701 | |
plotMutualFindings | 1.213 | 0.032 | 1.244 | |
plotPositives | 0.795 | 0.012 | 0.807 | |
plotQQ | 2.185 | 0.016 | 2.200 | |
plotRMSE | 1.947 | 0.064 | 2.011 | |
prepareObserved | 0.001 | 0.000 | 0.001 | |
runDA | 0.519 | 0.000 | 0.520 | |
runMocks | 0.752 | 0.000 | 0.753 | |
runNormalizations | 0.518 | 0.000 | 0.518 | |
runSplits | 3.819 | 0.100 | 3.919 | |
setNormalizations | 0 | 0 | 0 | |
set_ALDEx2 | 0.008 | 0.000 | 0.008 | |
set_ANCOM | 0.008 | 0.000 | 0.008 | |
set_DESeq2 | 0.008 | 0.000 | 0.008 | |
set_MAST | 0.003 | 0.000 | 0.003 | |
set_NOISeq | 0.003 | 0.000 | 0.003 | |
set_Seurat | 0.006 | 0.000 | 0.006 | |
set_basic | 0.002 | 0.000 | 0.002 | |
set_corncob | 0.004 | 0.000 | 0.004 | |
set_dearseq | 0.002 | 0.000 | 0.002 | |
set_edgeR | 0.012 | 0.000 | 0.012 | |
set_limma | 0.008 | 0.000 | 0.008 | |
set_metagenomeSeq | 0.005 | 0.000 | 0.005 | |
weights_ZINB | 0.428 | 0.000 | 0.428 | |